Hi, I just wanted to chime in on this. I did a firmware update this past weekend and ran into the issues, and I couldn't find a whole lot of relevant information except for this post.
My company inherited support of a MFSYS25 with 4 compute modules. Firmware was at 2.7. We had an issue a while back of the thing locking up when we attempted to power on the compute modules through the management interface, and Intel's suggestion was to update the firmware. I updated it to 6.8, which although it's a big jump, it was documented as an okay path to go, and support assured me it was good. I opted to not do 6.9 since I had already been looking into 6.8 for a bit.
Basically, things were going pretty smoothly until the BIOS updates to the compute modules was the next step, and all four of them would post. Just like the OP, I was able to get two of them going after simply using the jumper on board to reset the CMOS. The other two, I'm honestly not sure what it was that fixed them. I reset the CMOS a few times, and tried another jumper for the recovery BIOS, to no avail. I tried different combinations of pushing the power button and powering on through the interface as well. After a couple hours of trying, I had another person remote in to look at it. He simply clicked the link to reset one, and it did the BIOS updated and then booted up. The other, which was powered off, he clicked the link to power on, and this one too then went flawlessly. These were steps I had already tried, so I'm not sure what it was that caused it to work that time (perhaps letting them sit for a while did it?).
I write this just incase any others run into problems and happen across this.